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NM_000334.4(SCN4A):c.4360C>T (p.Arg1454Trp) AND Congenital myasthenic syndrome 16

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
May 7, 2022
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002512068.11

Allele description [Variation Report for NM_000334.4(SCN4A):c.4360C>T (p.Arg1454Trp)]

NM_000334.4(SCN4A):c.4360C>T (p.Arg1454Trp)

Genes:
GH-LCR:growth hormone locus control region [Gene]
SCN4A:sodium voltage-gated channel alpha subunit 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q23.3
Genomic location:
Preferred name:
NM_000334.4(SCN4A):c.4360C>T (p.Arg1454Trp)
HGVS:
  • NC_000017.11:g.63941922G>A
  • NG_011699.1:g.35997C>T
  • NG_042788.1:g.24830G>A
  • NM_000334.4:c.4360C>TMANE SELECT
  • NP_000325.4:p.Arg1454Trp
  • NP_000325.4:p.Arg1454Trp
  • NC_000017.10:g.62019282G>A
  • P35499:p.Arg1454Trp
Protein change:
R1454W; ARG1454TRP
Links:
UniProtKB: P35499#VAR_075436; OMIM: 603967.0041; dbSNP: rs879253789
NCBI 1000 Genomes Browser:
rs879253789
Molecular consequence:
  • NM_000334.4:c.4360C>T - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
loss_of_function_variant [Sequence Ontology: SO:0002054]
Observations:
1

Condition(s)

Name:
Congenital myasthenic syndrome 16
Synonyms:
Congenital myasthenic syndrome, acetazolamide-responsive
Identifiers:
MONDO: MONDO:0013620; MedGen: C3280112; Orphanet: 590; OMIM: 614198

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002549165Experimental Epileptology, AG Lerche, Hertie Institute for Clinical Brain Research
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(May 7, 2022)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV003924058OMIM
no assertion criteria provided
Pathogenic
(Jul 16, 2024)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

A recessive Nav1.4 mutation underlies congenital myasthenic syndrome with periodic paralysis.

Habbout K, Poulin H, Rivier F, Giuliano S, Sternberg D, Fontaine B, Eymard B, Morales RJ, Echenne B, King L, Hanna MG, Männikkö R, Chahine M, Nicole S, Bendahhou S.

Neurology. 2016 Jan 12;86(2):161-9. doi: 10.1212/WNL.0000000000002264. Epub 2015 Dec 11.

PubMed [citation]
PMID:
26659129
PMCID:
PMC4731685
See all PubMed Citations (3)

Details of each submission

From Experimental Epileptology, AG Lerche, Hertie Institute for Clinical Brain Research, SCV002549165.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (2)

Description

The variant was identified using whole exome sequencing and validated using Sanger sequencing.

Description

The variant SCN4A:p.(R1454W) has been identified in compound heterozyous state with a previously unreported variant SCN4A:p.(N1205K). It has an extremely low frequency in gnomAD r2.1 (MAF = 0.00001609 and no homozygotes). It is located in the voltage sensor domain (S4) which is a mutational hotspot and multiple lines of computational evidence support a deleterious effect (CADD: 25.9, GERP++: 2.7, PPh2: 0.99, SIFT: 0). It was first reported in homozygous state in an individual who suffered from muscle weakness consistent with a diagnosis of autosomal recessive Congenital Myasthenic Syndrome 16 (MIM: #614198). Functional characterization in a heterologous expression system showed a net loss of funtion with enhanced fast and slow inactivation with slow recovery (PMID: 26659129). It was therefore classified as likely pathogenic (ACMG/AMP criteria: PS3, PM1, PM2, PP3).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From OMIM, SCV003924058.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

Congenital Myasthenic Syndrome 16

In a 26-year-old Lebanese woman, born of consanguineous parents, with congenital myasthenic syndrome-16 (CMS16; 614198), Habbout et al. (2016) identified a homozygous c.4360C-T transition (c.4360C-T, NM_000334.4) in exon 24 of the SCN4A gene, resulting in an arg1454-to-trp (R1454W) substitution in the DIVS4 domain. Each unaffected parent was heterozygous for the mutation. In vitro functional expression studies showed that the mutation resulted in a loss-of-function effect, with slowed current decay, slowed fast inactivation, and increased activation time compared to wildtype. Slowed inactivation was also disturbed. Current density was not affected, but there was a decrease in current amplitude in response to repetitive stimulation above 10 Hz. The findings thus showed a combination of gating behaviors that favor the inactivation state; defective inactivation may induce fatigable weakness during muscle firing. The phenotype in this patient comprised both CMS and normokalemic periodic paralysis.

Classic Congenital Myopathy 22A

For discussion of the c.4360C-T transition in the SCN4A gene, resulting in an R1454W mutation, that was found in compound heterozygous state in a patient with classic congenital myopathy-22A (CMYO22A; 620351) by Berghold et al. (2022), see 603967.0042. Berghold et al. (2022) noted that the R1454W variant was present at a low frequency (1.6 x 10(-5)) in heterozygous state in the gnomAD database.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 26, 2024